Language issues

1. I was raised as a 100% R guy (i.e., I’d only heard of MATLAB)

global POP_LOGML

if ready == 0
  if vaihe == 1
    roundTypes = [1];
  elseif vaihe == 2
    roundTypes = [2 1];
  elseif vaihe == 3
    roundTypes = [5 5 7];
  elseif vaihe == 4
    roundTypes = [4 3 1];
  elseif vaihe == 5
    roundTypes = [6 7 2 3 4 1];
  end
end

% TALLENNETAAN
npops = poistaTyhjatPopulaatiot(npops);

The legacy

The plan

1. Run the original BAPS to get acquainted
2. Translate software to R, acquire XP on the go
3. Publish when it’s ready (“5k LOC? Should take a couple of years, LOL”)

Getting the original BAPS to run

• Can’t run the old binaries
• Can’t recompile the source code (skill issue)
  • Eventually got the original working in Jan 2024
  • Before then, much manual running of single MATLAB functions (bottom-up)
• Even after running original, demo data wouldn’t run (version issue somewhere, probably)

Top-down vs. bottom-up programming

Go from top-level functions down the rabbit hole or the other way around?

1. Started bottom-up
2. Got annoyed at 🐢 development speed, switched
3. Things broke spectacularly, switched back.

Coming to grips with an alien language and its IDE

<rant><matlab>

“WTF are these shortcuts? Alt+WAlt+W to copy? Ctrl+YCtrl+Y pastes?”

MATLAB is just weird (for an R user)

• No default values for function arguments?
• “WTF is this nargin()?”
• Inconsistent behavior w.r.t. “holy R”

MATLAB subsets are just weird

if testaaPop(line3)==1
  %2 rivi tällöin lokusrivi
  nloci = rivinSisaltamienMjonojenLkm(line2);
  line4 = fgetl(fid);
  if isequal(line4,-1)
      disp('Incorrect file format'); fclose(fid);
      return
  end
  if ~any(line4==',')
      % Rivin nelj?täytyy sisältää pilkku.
      disp('Incorrect file format'); fclose(fid);
      return
  end
  pointer = 1;
  while ~isequal(line4(pointer),',')  %Tiedetään, ett?pysähtyy
      pointer = pointer+1;
  end
  line4 = line4(pointer+1:end);  %pilkun jälkeinen osa
  nloci2 = rivinSisaltamienMjonojenLkm(line4);
  if (nloci2~=nloci)
      disp('Incorrect file format'); fclose(fid);
      return
  end
end

MATLAB assignments are also weird

>> 10:-1:1

ans =

    10     9     8     7     6     5     4     3     2     1

MATLAB assignments are also weird

>> 10:-1:1

ans =

    10     9     8     7     6     5     4     3     2     1

>> a = max(10:-1:1)

a =

    10

>> [a, b] = max(10:-1:1)

a =

    10


b =

     1

Homonymous functions can work differently

>> A = [1 2 3; 4 5 6]

A =

     1     2     3
     4     5     6

R> (A <- matrix(c(1, 4, 2, 5, 3, 6), 2))
     [,1] [,2] [,3]
[1,]    1    2    3
[2,]    4    5    6

>> sum(A)

ans =

     5     7     9

R> sum(A)
[1] 21

R vectors are just weird

(x <- c(11, 22, 33))

[1] 11 22 33

(tx <- t(c(11, 22, 33)))

     [,1] [,2] [,3]
[1,]   11   22   33

“So x is not even a row vector?”

R vectors are just weird

(x <- c(11, 22, 33))

[1] 11 22 33

(tx <- t(c(11, 22, 33)))

     [,1] [,2] [,3]
[1,]   11   22   33

dim(x)

NULL

dim(tx)

[1] 1 3

R vectors are just weird

(x <- c(11, 22, 33))

[1] 11 22 33

(tx <- t(c(11, 22, 33)))

     [,1] [,2] [,3]
[1,]   11   22   33

dim(x)

NULL

dim(tx)

[1] 1 3

class(x)

[1] "numeric"

class(tx)

[1] "matrix" "array" 

R vectors are just weird

(x <- c(11, 22, 33))

[1] 11 22 33

(tx <- t(c(11, 22, 33)))

     [,1] [,2] [,3]
[1,]   11   22   33

dim(x)

NULL

dim(tx)

[1] 1 3

class(x)

[1] "numeric"

class(tx)

[1] "matrix" "array" 

Or maybe it’s just the way we rely on c() instead of matrix() for creating vectors?

Nope. “Core R” does it too:

(A <- matrix(11:19, nrow = 3))

     [,1] [,2] [,3]
[1,]   11   14   17
[2,]   12   15   18
[3,]   13   16   19

class(A[2, ])

[1] "integer"

No, not "double" as before. Don’t get me started on R’s dynamic typing shenanigans.

Nope. “Core R” does it too:

(A <- matrix(11:19, nrow = 3))

     [,1] [,2] [,3]
[1,]   11   14   17
[2,]   12   15   18
[3,]   13   16   19

class(A[2, ])

[1] "integer"

class(A[2, , drop = FALSE])

[1] "matrix" "array" 

</r></rant>

Porting packages is harder than scripts (well, duh)

• No idea about how scopes on MATLAB packages work
• But I could see lots of duplicated/overloaded functions
• So 5 kLOC became much more

1. Publishing papers vs. software

Understand and disseminate the differences.

• Make your MVP as M as possible (4 modules is 3 too many; no extras)
• Don’t give estimates (or give it in hundreds of hours, if you must)
• Release ASAP to avoid overhype
• …but also take it slow and steady
• No such thing as bug-free software
• “Art can’t be finished, only abandoned” (Leonardo da Vinci?)

2. Don’t hate the language, hate the IDE

• Use whatever tool works best for you (even Emacs)
• But don’t be afraid to explore new things!
  • 2005-2019: “R and RStudio are all I care about”
  • 2020-2024: “I love all languages (even MATLAB). VSC and vim are all I need!”
  • 20XX: ?

3. Future-proof your ideas: make them public

Github: wleoncio, ocbe-uio